BRB OSCC Strain Analysis
J Zhao & J Bisanz
2024-09-11 14:09
1 Setup
library(tidyverse)
library(readxl) # read_excel
library(qiime2R) # theme_q2r
library(ggplot2)
library(dplyr)
library(readr) # read_csv
library(tidyr)
library(growthcurver)
library(drc)
library(vegan) # PCA adonis
library(tibble) # column_to_rownames()
library(tidyquant) #tq_mutate
library(ggtree) # read.tree
library(tidytree) # drop.tip
#Set working directory
setwd("/home/jjz5561/BRB_Mar2024/CAPR_computation/")
getwd()## [1] "/home/jjz5561/BRB_Mar2024/CAPR_computation"sessionInfo()## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 20.04.6 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] tidytree_0.4.6 ggtree_3.12.0
## [3] tidyquant_1.0.7 quantmod_0.4.26
## [5] TTR_0.24.4 PerformanceAnalytics_2.0.4
## [7] xts_0.14.0 zoo_1.8-12
## [9] vegan_2.6-6.1 lattice_0.22-6
## [11] permute_0.9-7 drc_3.0-1
## [13] MASS_7.3-61 growthcurver_0.3.1
## [15] qiime2R_0.99.6 readxl_1.4.3
## [17] lubridate_1.9.3 forcats_1.0.0
## [19] stringr_1.5.1 dplyr_1.1.4
## [21] purrr_1.0.2 readr_2.1.5
## [23] tidyr_1.3.1 tibble_3.2.1
## [25] ggplot2_3.5.1 tidyverse_2.0.0
##
## loaded via a namespace (and not attached):
## [1] rstudioapi_0.16.0 jsonlite_1.8.8 magrittr_2.0.3
## [4] TH.data_1.1-2 NADA_1.6-1.1 rmarkdown_2.27
## [7] fs_1.6.4 zlibbioc_1.50.0 vctrs_0.6.5
## [10] multtest_2.60.0 memoise_2.0.1 base64enc_0.1-3
## [13] htmltools_0.5.8.1 plotrix_3.8-4 curl_5.2.1
## [16] truncnorm_1.0-9 cellranger_1.1.0 Rhdf5lib_1.26.0
## [19] gridGraphics_0.5-1 Formula_1.2-5 rhdf5_2.48.0
## [22] sass_0.4.9 bslib_0.8.0 htmlwidgets_1.6.4
## [25] plyr_1.8.9 sandwich_3.1-0 cachem_1.1.0
## [28] igraph_2.0.3 lifecycle_1.0.4 iterators_1.0.14
## [31] pkgconfig_2.0.3 Matrix_1.7-0 R6_2.5.1
## [34] fastmap_1.2.0 GenomeInfoDbData_1.2.12 aplot_0.2.3
## [37] digest_0.6.36 colorspace_2.1-1 patchwork_1.2.0
## [40] S4Vectors_0.42.1 Hmisc_5.1-3 fansi_1.0.6
## [43] timechange_0.3.0 httr_1.4.7 abind_1.4-5
## [46] mgcv_1.9-1 compiler_4.4.1 withr_3.0.1
## [49] htmlTable_2.4.3 backports_1.5.0 carData_3.0-5
## [52] Quandl_2.11.0 biomformat_1.32.0 gtools_3.9.5
## [55] tools_4.4.1 foreign_0.8-86 ape_5.8
## [58] nnet_7.3-19 glue_1.7.0 quadprog_1.5-8
## [61] nlme_3.1-166 rhdf5filters_1.16.0 grid_4.4.1
## [64] checkmate_2.3.2 cluster_2.1.6 reshape2_1.4.4
## [67] ade4_1.7-22 generics_0.1.3 gtable_0.3.5
## [70] tzdb_0.4.0 data.table_1.15.4 hms_1.1.3
## [73] car_3.1-2 utf8_1.2.4 XVector_0.44.0
## [76] BiocGenerics_0.50.0 foreach_1.5.2 pillar_1.9.0
## [79] yulab.utils_0.1.5 splines_4.4.1 treeio_1.28.0
## [82] survival_3.7-0 tidyselect_1.2.1 Biostrings_2.72.1
## [85] knitr_1.48 gridExtra_2.3 phyloseq_1.48.0
## [88] IRanges_2.38.1 zCompositions_1.5.0-4 stats4_4.4.1
## [91] xfun_0.46 Biobase_2.64.0 DT_0.33
## [94] stringi_1.8.4 UCSC.utils_1.0.0 ggfun_0.1.5
## [97] lazyeval_0.2.2 yaml_2.3.10 evaluate_0.24.0
## [100] codetools_0.2-20 ggplotify_0.1.2 cli_3.6.3
## [103] rpart_4.1.23 munsell_0.5.1 jquerylib_0.1.4
## [106] Rcpp_1.0.13 GenomeInfoDb_1.40.1 parallel_4.4.1
## [109] mvtnorm_1.2-5 scales_1.3.0 crayon_1.5.3
## [112] rlang_1.1.4 multcomp_1.4-26theme_set(theme_q2r())1.1 Citation Information
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## [[27]]
## To cite Formula in publications use:
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## Zeileis A, Croissant Y (2010). "Extended Model Formulas in R:
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## number = {1},
## pages = {1--13},
## doi = {10.18637/jss.v034.i01},
## }
##
## [[28]]
## To cite package 'rhdf5' in publications use:
##
## Fischer B, Smith M, Pau G (2024). _rhdf5: R Interface to HDF5_.
## doi:10.18129/B9.bioc.rhdf5 <https://doi.org/10.18129/B9.bioc.rhdf5>,
## R package version 2.48.0, <https://bioconductor.org/packages/rhdf5>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {rhdf5: R Interface to HDF5},
## author = {Bernd Fischer and Mike Smith and Gregoire Pau},
## year = {2024},
## note = {R package version 2.48.0},
## url = {https://bioconductor.org/packages/rhdf5},
## doi = {10.18129/B9.bioc.rhdf5},
## }
##
## [[29]]
## To cite package 'sass' in publications use:
##
## Cheng J, Mastny T, Iannone R, Schloerke B, Sievert C (2024). _sass:
## Syntactically Awesome Style Sheets ('Sass')_. R package version
## 0.4.9, <https://CRAN.R-project.org/package=sass>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {sass: Syntactically Awesome Style Sheets ('Sass')},
## author = {Joe Cheng and Timothy Mastny and Richard Iannone and Barret Schloerke and Carson Sievert},
## year = {2024},
## note = {R package version 0.4.9},
## url = {https://CRAN.R-project.org/package=sass},
## }
##
## [[30]]
## To cite package 'bslib' in publications use:
##
## Sievert C, Cheng J, Aden-Buie G (2024). _bslib: Custom 'Bootstrap'
## 'Sass' Themes for 'shiny' and 'rmarkdown'_. R package version 0.8.0,
## <https://CRAN.R-project.org/package=bslib>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {bslib: Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'},
## author = {Carson Sievert and Joe Cheng and Garrick Aden-Buie},
## year = {2024},
## note = {R package version 0.8.0},
## url = {https://CRAN.R-project.org/package=bslib},
## }
##
## [[31]]
## To cite package 'htmlwidgets' in publications use:
##
## Vaidyanathan R, Xie Y, Allaire J, Cheng J, Sievert C, Russell K
## (2023). _htmlwidgets: HTML Widgets for R_. R package version 1.6.4,
## <https://CRAN.R-project.org/package=htmlwidgets>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {htmlwidgets: HTML Widgets for R},
## author = {Ramnath Vaidyanathan and Yihui Xie and JJ Allaire and Joe Cheng and Carson Sievert and Kenton Russell},
## year = {2023},
## note = {R package version 1.6.4},
## url = {https://CRAN.R-project.org/package=htmlwidgets},
## }
##
## [[32]]
## To cite package 'plyr' in publications use:
##
## Hadley Wickham (2011). The Split-Apply-Combine Strategy for Data
## Analysis. Journal of Statistical Software, 40(1), 1-29. URL
## https://www.jstatsoft.org/v40/i01/.
##
## A BibTeX entry for LaTeX users is
##
## @Article{,
## title = {The Split-Apply-Combine Strategy for Data Analysis},
## author = {Hadley Wickham},
## journal = {Journal of Statistical Software},
## year = {2011},
## volume = {40},
## number = {1},
## pages = {1--29},
## url = {https://www.jstatsoft.org/v40/i01/},
## }
##
## [[33]]
## To cite sandwich in publications use:
##
## Zeileis A, Köll S, Graham N (2020). "Various Versatile Variances: An
## Object-Oriented Implementation of Clustered Covariances in R."
## _Journal of Statistical Software_, *95*(1), 1-36.
## doi:10.18637/jss.v095.i01 <https://doi.org/10.18637/jss.v095.i01>.
##
## If sandwich is applied to lm() models, please also cite:
##
## Zeileis A (2004). "Econometric Computing with HC and HAC Covariance
## Matrix Estimators." _Journal of Statistical Software_, *11*(10),
## 1-17. doi:10.18637/jss.v011.i10
## <https://doi.org/10.18637/jss.v011.i10>.
##
## If sandwich is applied to models other than lm(), please also cite:
##
## Zeileis A (2006). "Object-Oriented Computation of Sandwich
## Estimators." _Journal of Statistical Software_, *16*(9), 1-16.
## doi:10.18637/jss.v016.i09 <https://doi.org/10.18637/jss.v016.i09>.
##
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.
##
## [[34]]
## To cite package 'cachem' in publications use:
##
## Chang W (2024). _cachem: Cache R Objects with Automatic Pruning_. R
## package version 1.1.0, <https://CRAN.R-project.org/package=cachem>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {cachem: Cache R Objects with Automatic Pruning},
## author = {Winston Chang},
## year = {2024},
## note = {R package version 1.1.0},
## url = {https://CRAN.R-project.org/package=cachem},
## }
##
## [[35]]
## To cite 'igraph' in publications use:
##
## Csardi G, Nepusz T (2006). "The igraph software package for complex
## network research." _InterJournal_, *Complex Systems*, 1695.
## <https://igraph.org>.
##
## Csárdi G, Nepusz T, Traag V, Horvát Sz, Zanini F, Noom D, Müller K
## (2024). _igraph: Network Analysis and Visualization in R_.
## doi:10.5281/zenodo.7682609 <https://doi.org/10.5281/zenodo.7682609>, R
## package version 2.0.3, <https://CRAN.R-project.org/package=igraph>.
##
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.
##
## [[36]]
## To cite package 'lifecycle' in publications use:
##
## Henry L, Wickham H (2023). _lifecycle: Manage the Life Cycle of your
## Package Functions_. R package version 1.0.4,
## <https://CRAN.R-project.org/package=lifecycle>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {lifecycle: Manage the Life Cycle of your Package Functions},
## author = {Lionel Henry and Hadley Wickham},
## year = {2023},
## note = {R package version 1.0.4},
## url = {https://CRAN.R-project.org/package=lifecycle},
## }
##
## [[37]]
## To cite package 'iterators' in publications use:
##
## Analytics R, Weston S (2022). _iterators: Provides Iterator
## Construct_. R package version 1.0.14,
## <https://CRAN.R-project.org/package=iterators>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {iterators: Provides Iterator Construct},
## author = {Revolution Analytics and Steve Weston},
## year = {2022},
## note = {R package version 1.0.14},
## url = {https://CRAN.R-project.org/package=iterators},
## }
##
## [[38]]
## To cite package 'pkgconfig' in publications use:
##
## Csárdi G (2019). _pkgconfig: Private Configuration for 'R' Packages_.
## R package version 2.0.3,
## <https://CRAN.R-project.org/package=pkgconfig>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {pkgconfig: Private Configuration for 'R' Packages},
## author = {Gábor Csárdi},
## year = {2019},
## note = {R package version 2.0.3},
## url = {https://CRAN.R-project.org/package=pkgconfig},
## }
##
## ATTENTION: This citation information has been auto-generated from the
## package DESCRIPTION file and may need manual editing, see
## 'help("citation")'.
##
## [[39]]
## To cite package 'Matrix' in publications use:
##
## Bates D, Maechler M, Jagan M (2024). _Matrix: Sparse and Dense Matrix
## Classes and Methods_. R package version 1.7-0,
## <https://CRAN.R-project.org/package=Matrix>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {Matrix: Sparse and Dense Matrix Classes and Methods},
## author = {Douglas Bates and Martin Maechler and Mikael Jagan},
## year = {2024},
## note = {R package version 1.7-0},
## url = {https://CRAN.R-project.org/package=Matrix},
## }
##
## [[40]]
## To cite package 'R6' in publications use:
##
## Chang W (2021). _R6: Encapsulated Classes with Reference Semantics_.
## R package version 2.5.1, <https://CRAN.R-project.org/package=R6>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {R6: Encapsulated Classes with Reference Semantics},
## author = {Winston Chang},
## year = {2021},
## note = {R package version 2.5.1},
## url = {https://CRAN.R-project.org/package=R6},
## }
##
## [[41]]
## To cite package 'fastmap' in publications use:
##
## Chang W (2024). _fastmap: Fast Data Structures_. R package version
## 1.2.0, <https://CRAN.R-project.org/package=fastmap>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {fastmap: Fast Data Structures},
## author = {Winston Chang},
## year = {2024},
## note = {R package version 1.2.0},
## url = {https://CRAN.R-project.org/package=fastmap},
## }
##
## [[42]]
## To cite package 'GenomeInfoDbData' in publications use:
##
## Team BC (2024). _GenomeInfoDbData: Species and taxonomy ID look up
## tables used by GenomeInfoDb_. R package version 1.2.12.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {GenomeInfoDbData: Species and taxonomy ID look up tables used by GenomeInfoDb},
## author = {Bioconductor Core Team},
## year = {2024},
## note = {R package version 1.2.12},
## }
##
## ATTENTION: This citation information has been auto-generated from the
## package DESCRIPTION file and may need manual editing, see
## 'help("citation")'.
##
## [[43]]
## To cite package 'aplot' in publications use:
##
## Yu G (2024). _aplot: Decorate a 'ggplot' with Associated
## Information_. R package version 0.2.3,
## <https://CRAN.R-project.org/package=aplot>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {aplot: Decorate a 'ggplot' with Associated Information},
## author = {Guangchuang Yu},
## year = {2024},
## note = {R package version 0.2.3},
## url = {https://CRAN.R-project.org/package=aplot},
## }
##
## [[44]]
## To cite package 'digest' in publications use:
##
## Lucas DEwcbA, Tuszynski J, Bengtsson H, Urbanek S, Frasca M, Lewis B,
## Stokely M, Muehleisen H, Murdoch D, Hester J, Wu W, Kou Q, Onkelinx
## T, Lang M, Simko V, Hornik K, Neal R, Bell K, de Queljoe M, Suruceanu
## I, Denney B, Schumacher D, Chang W, Attali D, Chirico. M (2024).
## _digest: Create Compact Hash Digests of R Objects_. R package version
## 0.6.36, <https://CRAN.R-project.org/package=digest>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {digest: Create Compact Hash Digests of R Objects},
## author = {Dirk Eddelbuettel with contributions by Antoine Lucas and Jarek Tuszynski and Henrik Bengtsson and Simon Urbanek and Mario Frasca and Bryan Lewis and Murray Stokely and Hannes Muehleisen and Duncan Murdoch and Jim Hester and Wush Wu and Qiang Kou and Thierry Onkelinx and Michel Lang and Viliam Simko and Kurt Hornik and Radford Neal and Kendon Bell and Matthew {de Queljoe} and Ion Suruceanu and Bill Denney and Dirk Schumacher and Winston Chang and Dean Attali and Michael Chirico.},
## year = {2024},
## note = {R package version 0.6.36},
## url = {https://CRAN.R-project.org/package=digest},
## }
##
## ATTENTION: This citation information has been auto-generated from the
## package DESCRIPTION file and may need manual editing, see
## 'help("citation")'.
##
## [[45]]
## To cite colorspace in publications use:
##
## Zeileis A, Fisher JC, Hornik K, Ihaka R, McWhite CD, Murrell P,
## Stauffer R, Wilke CO (2020). "colorspace: A Toolbox for Manipulating
## and Assessing Colors and Palettes." _Journal of Statistical
## Software_, *96*(1), 1-49. doi:10.18637/jss.v096.i01
## <https://doi.org/10.18637/jss.v096.i01>.
##
## If you use HCL-based color palettes, please cite:
##
## Zeileis A, Hornik K, Murrell P (2009). "Escaping RGBland: Selecting
## Colors for Statistical Graphics." _Computational Statistics & Data
## Analysis_, *53*(9), 3259-3270. doi:10.1016/j.csda.2008.11.033
## <https://doi.org/10.1016/j.csda.2008.11.033>.
##
## If you use HCL-based color palettes in meteorological visualizations,
## please cite:
##
## Stauffer R, Mayr GJ, Dabernig M, Zeileis A (2009). "Somewhere over
## the Rainbow: How to Make Effective Use of Colors in Meteorological
## Visualizations." _Bulletin of the American Meteorological Society_,
## *96*(2), 203-216. doi:10.1175/BAMS-D-13-00155.1
## <https://doi.org/10.1175/BAMS-D-13-00155.1>.
##
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.
##
## [[46]]
## To cite package 'patchwork' in publications use:
##
## Pedersen T (2024). _patchwork: The Composer of Plots_. R package
## version 1.2.0, <https://CRAN.R-project.org/package=patchwork>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {patchwork: The Composer of Plots},
## author = {Thomas Lin Pedersen},
## year = {2024},
## note = {R package version 1.2.0},
## url = {https://CRAN.R-project.org/package=patchwork},
## }
##
## [[47]]
## To cite package 'S4Vectors' in publications use:
##
## Pagès H, Lawrence M, Aboyoun P (2024). _S4Vectors: Foundation of
## vector-like and list-like containers in Bioconductor_.
## doi:10.18129/B9.bioc.S4Vectors
## <https://doi.org/10.18129/B9.bioc.S4Vectors>, R package version
## 0.42.1, <https://bioconductor.org/packages/S4Vectors>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {S4Vectors: Foundation of vector-like and list-like containers in
## Bioconductor},
## author = {Hervé Pagès and Michael Lawrence and Patrick Aboyoun},
## year = {2024},
## note = {R package version 0.42.1},
## url = {https://bioconductor.org/packages/S4Vectors},
## doi = {10.18129/B9.bioc.S4Vectors},
## }
##
## [[48]]
## To cite package 'Hmisc' in publications use:
##
## Harrell Jr F (2024). _Hmisc: Harrell Miscellaneous_. R package
## version 5.1-3, <https://CRAN.R-project.org/package=Hmisc>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {Hmisc: Harrell Miscellaneous},
## author = {Frank E {Harrell Jr}},
## year = {2024},
## note = {R package version 5.1-3},
## url = {https://CRAN.R-project.org/package=Hmisc},
## }
##
## [[49]]
## To cite package 'fansi' in publications use:
##
## Gaslam B (2023). _fansi: ANSI Control Sequence Aware String
## Functions_. R package version 1.0.6,
## <https://CRAN.R-project.org/package=fansi>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {fansi: ANSI Control Sequence Aware String Functions},
## author = {Brodie Gaslam},
## year = {2023},
## note = {R package version 1.0.6},
## url = {https://CRAN.R-project.org/package=fansi},
## }
##
## [[50]]
## To cite package 'timechange' in publications use:
##
## Spinu V (2024). _timechange: Efficient Manipulation of Date-Times_. R
## package version 0.3.0,
## <https://CRAN.R-project.org/package=timechange>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {timechange: Efficient Manipulation of Date-Times},
## author = {Vitalie Spinu},
## year = {2024},
## note = {R package version 0.3.0},
## url = {https://CRAN.R-project.org/package=timechange},
## }
##
## [[51]]
## To cite package 'httr' in publications use:
##
## Wickham H (2023). _httr: Tools for Working with URLs and HTTP_. R
## package version 1.4.7, <https://CRAN.R-project.org/package=httr>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {httr: Tools for Working with URLs and HTTP},
## author = {Hadley Wickham},
## year = {2023},
## note = {R package version 1.4.7},
## url = {https://CRAN.R-project.org/package=httr},
## }
##
## [[52]]
## To cite package 'abind' in publications use:
##
## Plate T, Heiberger R (2016). _abind: Combine Multidimensional
## Arrays_. R package version 1.4-5,
## <https://CRAN.R-project.org/package=abind>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {abind: Combine Multidimensional Arrays},
## author = {Tony Plate and Richard Heiberger},
## year = {2016},
## note = {R package version 1.4-5},
## url = {https://CRAN.R-project.org/package=abind},
## }
##
## ATTENTION: This citation information has been auto-generated from the
## package DESCRIPTION file and may need manual editing, see
## 'help("citation")'.
##
## [[53]]
## 2011 for generalized additive model method; 2016 for beyond exponential
## family; 2004 for strictly additive GCV based model method and basics of
## gamm; 2017 for overview; 2003 for thin plate regression splines.
##
## Wood, S.N. (2011) Fast stable restricted maximum likelihood and
## marginal likelihood estimation of semiparametric generalized linear
## models. Journal of the Royal Statistical Society (B) 73(1):3-36
##
## Wood S.N., N. Pya and B. Saefken (2016) Smoothing parameter and model
## selection for general smooth models (with discussion). Journal of the
## American Statistical Association 111:1548-1575.
##
## Wood, S.N. (2004) Stable and efficient multiple smoothing parameter
## estimation for generalized additive models. Journal of the American
## Statistical Association. 99:673-686.
##
## Wood, S.N. (2017) Generalized Additive Models: An Introduction with R
## (2nd edition). Chapman and Hall/CRC.
##
## Wood, S.N. (2003) Thin-plate regression splines. Journal of the Royal
## Statistical Society (B) 65(1):95-114.
##
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.
##
## [[54]]
## The 'compiler' package is part of R. To cite R in publications use:
##
## R Core Team (2024). _R: A Language and Environment for Statistical
## Computing_. R Foundation for Statistical Computing, Vienna, Austria.
## <https://www.R-project.org/>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {R: A Language and Environment for Statistical Computing},
## author = {{R Core Team}},
## organization = {R Foundation for Statistical Computing},
## address = {Vienna, Austria},
## year = {2024},
## url = {https://www.R-project.org/},
## }
##
## We have invested a lot of time and effort in creating R, please cite it
## when using it for data analysis. See also 'citation("pkgname")' for
## citing R packages.
##
## [[55]]
## To cite package 'withr' in publications use:
##
## Hester J, Henry L, Müller K, Ushey K, Wickham H, Chang W (2024).
## _withr: Run Code 'With' Temporarily Modified Global State_. R package
## version 3.0.1, <https://CRAN.R-project.org/package=withr>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {withr: Run Code 'With' Temporarily Modified Global State},
## author = {Jim Hester and Lionel Henry and Kirill Müller and Kevin Ushey and Hadley Wickham and Winston Chang},
## year = {2024},
## note = {R package version 3.0.1},
## url = {https://CRAN.R-project.org/package=withr},
## }
##
## [[56]]
## To cite package 'htmlTable' in publications use:
##
## Gordon M, Gragg S, Konings P (2024). _htmlTable: Advanced Tables for
## Markdown/HTML_. R package version 2.4.3,
## <https://CRAN.R-project.org/package=htmlTable>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {htmlTable: Advanced Tables for Markdown/HTML},
## author = {Max Gordon and Stephen Gragg and Peter Konings},
## year = {2024},
## note = {R package version 2.4.3},
## url = {https://CRAN.R-project.org/package=htmlTable},
## }
##
## [[57]]
## To cite package 'backports' in publications use:
##
## Lang M, Murdoch D, R Core Team (2024). _backports: Reimplementations
## of Functions Introduced Since R-3.0.0_. R package version 1.5.0,
## <https://CRAN.R-project.org/package=backports>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {backports: Reimplementations of Functions Introduced Since R-3.0.0},
## author = {Michel Lang and Duncan Murdoch and {R Core Team}},
## year = {2024},
## note = {R package version 1.5.0},
## url = {https://CRAN.R-project.org/package=backports},
## }
##
## [[58]]
## To cite package 'carData' in publications use:
##
## Fox J, Weisberg S, Price B (2022). _carData: Companion to Applied
## Regression Data Sets_. R package version 3.0-5,
## <https://CRAN.R-project.org/package=carData>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {carData: Companion to Applied Regression Data Sets},
## author = {John Fox and Sanford Weisberg and Brad Price},
## year = {2022},
## note = {R package version 3.0-5},
## url = {https://CRAN.R-project.org/package=carData},
## }
##
## [[59]]
## To cite package 'Quandl' in publications use:
##
## Raymond McTaggart, Gergely Daroczi, Clement Leung (2021). _Quandl:
## API Wrapper for Quandl.com_. R package version 2.11.0,
## <https://CRAN.R-project.org/package=Quandl>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {Quandl: API Wrapper for Quandl.com},
## author = {{Raymond McTaggart} and {Gergely Daroczi} and {Clement Leung}},
## year = {2021},
## note = {R package version 2.11.0},
## url = {https://CRAN.R-project.org/package=Quandl},
## }
##
## [[60]]
## To cite package 'biomformat' in publications use:
##
## McMurdie PJ, Paulson JN (2024). _biomformat: An interface package for
## the BIOM file format_. doi:10.18129/B9.bioc.biomformat
## <https://doi.org/10.18129/B9.bioc.biomformat>, R package version
## 1.32.0, <https://bioconductor.org/packages/biomformat>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {biomformat: An interface package for the BIOM file format},
## author = {Paul J. McMurdie and Joseph N Paulson},
## year = {2024},
## note = {R package version 1.32.0},
## url = {https://bioconductor.org/packages/biomformat},
## doi = {10.18129/B9.bioc.biomformat},
## }
##
## ATTENTION: This citation information has been auto-generated from the
## package DESCRIPTION file and may need manual editing, see
## 'help("citation")'.
##
## [[61]]
## To cite package 'gtools' in publications use:
##
## Warnes G, Bolker B, Lumley T, Magnusson A, Venables B, Ryodan G,
## Moeller S (2023). _gtools: Various R Programming Tools_. R package
## version 3.9.5, <https://CRAN.R-project.org/package=gtools>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {gtools: Various R Programming Tools},
## author = {Gregory R. Warnes and Ben Bolker and Thomas Lumley and Arni Magnusson and Bill Venables and Genei Ryodan and Steffen Moeller},
## year = {2023},
## note = {R package version 3.9.5},
## url = {https://CRAN.R-project.org/package=gtools},
## }
##
## [[62]]
## The 'tools' package is part of R. To cite R in publications use:
##
## R Core Team (2024). _R: A Language and Environment for Statistical
## Computing_. R Foundation for Statistical Computing, Vienna, Austria.
## <https://www.R-project.org/>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {R: A Language and Environment for Statistical Computing},
## author = {{R Core Team}},
## organization = {R Foundation for Statistical Computing},
## address = {Vienna, Austria},
## year = {2024},
## url = {https://www.R-project.org/},
## }
##
## We have invested a lot of time and effort in creating R, please cite it
## when using it for data analysis. See also 'citation("pkgname")' for
## citing R packages.
##
## [[63]]
## To cite package 'foreign' in publications use:
##
## R Core Team (2023). _foreign: Read Data Stored by 'Minitab', 'S',
## 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ..._. R package
## version 0.8-86, <https://CRAN.R-project.org/package=foreign>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {foreign: Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata',
## 'Systat', 'Weka', 'dBase', ...},
## author = {{R Core Team}},
## year = {2023},
## note = {R package version 0.8-86},
## url = {https://CRAN.R-project.org/package=foreign},
## }
##
## [[64]]
## To cite ape in a publication please use:
##
## Paradis E, Schliep K (2019). "ape 5.0: an environment for modern
## phylogenetics and evolutionary analyses in R." _Bioinformatics_,
## *35*, 526-528. doi:10.1093/bioinformatics/bty633
## <https://doi.org/10.1093/bioinformatics/bty633>.
##
## A BibTeX entry for LaTeX users is
##
## @Article{,
## title = {ape 5.0: an environment for modern phylogenetics and evolutionary analyses in {R}},
## author = {Emmanuel Paradis and Klaus Schliep},
## journal = {Bioinformatics},
## year = {2019},
## volume = {35},
## pages = {526-528},
## doi = {10.1093/bioinformatics/bty633},
## }
##
## ape is evolving quickly, so you may want to cite its version number
## (found with 'library(help = ape)' or 'packageVersion("ape")').
##
## [[65]]
## To cite the nnet package in publications use:
##
## Venables, W. N. & Ripley, B. D. (2002) Modern Applied Statistics with
## S. Fourth Edition. Springer, New York. ISBN 0-387-95457-0
##
## A BibTeX entry for LaTeX users is
##
## @Book{,
## title = {Modern Applied Statistics with S},
## author = {W. N. Venables and B. D. Ripley},
## publisher = {Springer},
## edition = {Fourth},
## address = {New York},
## year = {2002},
## note = {ISBN 0-387-95457-0},
## url = {https://www.stats.ox.ac.uk/pub/MASS4/},
## }
##
## [[66]]
## To cite package 'glue' in publications use:
##
## Hester J, Bryan J (2024). _glue: Interpreted String Literals_. R
## package version 1.7.0, <https://CRAN.R-project.org/package=glue>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {glue: Interpreted String Literals},
## author = {Jim Hester and Jennifer Bryan},
## year = {2024},
## note = {R package version 1.7.0},
## url = {https://CRAN.R-project.org/package=glue},
## }
##
## [[67]]
## To cite package 'quadprog' in publications use:
##
## dpodi/LINPACK) SobBATRpbAW<FcfCM (2019). _quadprog: Functions to
## Solve Quadratic Programming Problems_. R package version 1.5-8,
## <https://CRAN.R-project.org/package=quadprog>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {quadprog: Functions to Solve Quadratic Programming Problems},
## author = {S original by Berwin A. Turlach R port by Andreas Weingessel <Andreas.Weingessel@ci.tuwien.ac.at> Fortran contributions from Cleve Moler dpodi/LINPACK)},
## year = {2019},
## note = {R package version 1.5-8},
## url = {https://CRAN.R-project.org/package=quadprog},
## }
##
## ATTENTION: This citation information has been auto-generated from the
## package DESCRIPTION file and may need manual editing, see
## 'help("citation")'.
##
## [[68]]
## To cite package 'nlme' in publications use:
##
## Pinheiro J, Bates D, R Core Team (2024). _nlme: Linear and Nonlinear
## Mixed Effects Models_. R package version 3.1-166,
## <https://CRAN.R-project.org/package=nlme>.
##
## Pinheiro JC, Bates DM (2000). _Mixed-Effects Models in S and S-PLUS_.
## Springer, New York. doi:10.1007/b98882
## <https://doi.org/10.1007/b98882>.
##
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.
##
## [[69]]
## To cite package 'rhdf5filters' in publications use:
##
## Smith M (2024). _rhdf5filters: HDF5 Compression Filters_.
## doi:10.18129/B9.bioc.rhdf5filters
## <https://doi.org/10.18129/B9.bioc.rhdf5filters>, R package version
## 1.16.0, <https://bioconductor.org/packages/rhdf5filters>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {rhdf5filters: HDF5 Compression Filters},
## author = {Mike Smith},
## year = {2024},
## note = {R package version 1.16.0},
## url = {https://bioconductor.org/packages/rhdf5filters},
## doi = {10.18129/B9.bioc.rhdf5filters},
## }
##
## [[70]]
## The 'grid' package is part of R. To cite R in publications use:
##
## R Core Team (2024). _R: A Language and Environment for Statistical
## Computing_. R Foundation for Statistical Computing, Vienna, Austria.
## <https://www.R-project.org/>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {R: A Language and Environment for Statistical Computing},
## author = {{R Core Team}},
## organization = {R Foundation for Statistical Computing},
## address = {Vienna, Austria},
## year = {2024},
## url = {https://www.R-project.org/},
## }
##
## We have invested a lot of time and effort in creating R, please cite it
## when using it for data analysis. See also 'citation("pkgname")' for
## citing R packages.
##
## [[71]]
## To cite package 'checkmate' in publications use:
##
## Lang M (2017). "checkmate: Fast Argument Checks for Defensive R
## Programming." _The R Journal_, *9*(1), 437-445.
## doi:10.32614/RJ-2017-028 <https://doi.org/10.32614/RJ-2017-028>.
##
## A BibTeX entry for LaTeX users is
##
## @Article{checkmate,
## title = {{checkmate}: Fast Argument Checks for Defensive {R} Programming},
## author = {Michel Lang},
## journal = {The R Journal},
## year = {2017},
## doi = {10.32614/RJ-2017-028},
## pages = {437--445},
## volume = {9},
## number = {1},
## }
##
## [[72]]
## To cite the R package cluster in publications use:
##
## Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M., Hornik,
## K.(2023). cluster: Cluster Analysis Basics and Extensions. R package
## version 2.1.6.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {cluster: Cluster Analysis Basics and Extensions},
## author = {Martin Maechler and Peter Rousseeuw and Anja Struyf and Mia Hubert and Kurt Hornik},
## year = {2023},
## url = {https://CRAN.R-project.org/package=cluster},
## note = {R package version 2.1.6 --- For new features, see the 'NEWS' and the 'Changelog' file in the package source)},
## }
##
## [[73]]
## To cite reshape2 in publications use:
##
## Hadley Wickham (2007). Reshaping Data with the reshape Package.
## Journal of Statistical Software, 21(12), 1-20. URL
## http://www.jstatsoft.org/v21/i12/.
##
## A BibTeX entry for LaTeX users is
##
## @Article{,
## title = {Reshaping Data with the {reshape} Package},
## author = {Hadley Wickham},
## journal = {Journal of Statistical Software},
## year = {2007},
## volume = {21},
## number = {12},
## pages = {1--20},
## url = {http://www.jstatsoft.org/v21/i12/},
## }
##
## [[74]]
## To cite ade4 in publications use:
##
## Dray S, Dufour A (2007). "The ade4 Package: Implementing the Duality
## Diagram for Ecologists." _Journal of Statistical Software_, *22*(4),
## 1-20. doi:10.18637/jss.v022.i04
## <https://doi.org/10.18637/jss.v022.i04>.
##
## Bougeard S, Dray S (2018). "Supervised Multiblock Analysis in R with
## the ade4 Package." _Journal of Statistical Software_, *86*(1), 1-17.
## doi:10.18637/jss.v086.i01 <https://doi.org/10.18637/jss.v086.i01>.
##
## Chessel D, Dufour A, Thioulouse J (2004). "The ade4 Package - I:
## One-Table Methods." _R News_, *4*(1), 5-10.
## <https://cran.r-project.org/doc/Rnews/>.
##
## Dray S, Dufour A, Chessel D (2007). "The ade4 Package - II: Two-Table
## and K-Table Methods." _R News_, *7*(2), 47-52.
## <https://cran.r-project.org/doc/Rnews/>.
##
## Thioulouse J, Dray S, Dufour A, Siberchicot A, Jombart T, Pavoine S
## (2018). _Multivariate Analysis of Ecological Data with ade4_. Springer.
## doi:10.1007/978-1-4939-8850-1
## <https://doi.org/10.1007/978-1-4939-8850-1>.
##
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.
##
## [[75]]
## To cite package 'generics' in publications use:
##
## Wickham H, Kuhn M, Vaughan D (2022). _generics: Common S3 Generics
## not Provided by Base R Methods Related to Model Fitting_. R package
## version 0.1.3, <https://CRAN.R-project.org/package=generics>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {generics: Common S3 Generics not Provided by Base R Methods Related to
## Model Fitting},
## author = {Hadley Wickham and Max Kuhn and Davis Vaughan},
## year = {2022},
## note = {R package version 0.1.3},
## url = {https://CRAN.R-project.org/package=generics},
## }
##
## [[76]]
## To cite package 'gtable' in publications use:
##
## Wickham H, Pedersen T (2024). _gtable: Arrange 'Grobs' in Tables_. R
## package version 0.3.5, <https://CRAN.R-project.org/package=gtable>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {gtable: Arrange 'Grobs' in Tables},
## author = {Hadley Wickham and Thomas Lin Pedersen},
## year = {2024},
## note = {R package version 0.3.5},
## url = {https://CRAN.R-project.org/package=gtable},
## }
##
## [[77]]
## To cite package 'tzdb' in publications use:
##
## Vaughan D (2023). _tzdb: Time Zone Database Information_. R package
## version 0.4.0, <https://CRAN.R-project.org/package=tzdb>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {tzdb: Time Zone Database Information},
## author = {Davis Vaughan},
## year = {2023},
## note = {R package version 0.4.0},
## url = {https://CRAN.R-project.org/package=tzdb},
## }
##
## [[78]]
## To cite package 'data.table' in publications use:
##
## Barrett T, Dowle M, Srinivasan A, Gorecki J, Chirico M, Hocking T
## (2024). _data.table: Extension of `data.frame`_. R package version
## 1.15.4, <https://CRAN.R-project.org/package=data.table>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {data.table: Extension of `data.frame`},
## author = {Tyson Barrett and Matt Dowle and Arun Srinivasan and Jan Gorecki and Michael Chirico and Toby Hocking},
## year = {2024},
## note = {R package version 1.15.4},
## url = {https://CRAN.R-project.org/package=data.table},
## }
##
## [[79]]
## To cite package 'hms' in publications use:
##
## Müller K (2023). _hms: Pretty Time of Day_. R package version 1.1.3,
## <https://CRAN.R-project.org/package=hms>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {hms: Pretty Time of Day},
## author = {Kirill Müller},
## year = {2023},
## note = {R package version 1.1.3},
## url = {https://CRAN.R-project.org/package=hms},
## }
##
## [[80]]
## To cite the car package in publications use:
##
## Fox J, Weisberg S (2019). _An R Companion to Applied Regression_,
## Third edition. Sage, Thousand Oaks CA.
## <https://socialsciences.mcmaster.ca/jfox/Books/Companion/>.
##
## A BibTeX entry for LaTeX users is
##
## @Book{,
## title = {An {R} Companion to Applied Regression},
## edition = {Third},
## author = {John Fox and Sanford Weisberg},
## year = {2019},
## publisher = {Sage},
## address = {Thousand Oaks {CA}},
## url = {https://socialsciences.mcmaster.ca/jfox/Books/Companion/},
## }
##
## [[81]]
## To cite package 'utf8' in publications use:
##
## Perry PO (2023). _utf8: Unicode Text Processing_. R package version
## 1.2.4, <https://CRAN.R-project.org/package=utf8>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {utf8: Unicode Text Processing},
## author = {Patrick O. Perry},
## year = {2023},
## note = {R package version 1.2.4},
## url = {https://CRAN.R-project.org/package=utf8},
## }
##
## [[82]]
## To cite package 'XVector' in publications use:
##
## Pagès H, Aboyoun P (2024). _XVector: Foundation of external vector
## representation and manipulation in Bioconductor_.
## doi:10.18129/B9.bioc.XVector
## <https://doi.org/10.18129/B9.bioc.XVector>, R package version 0.44.0,
## <https://bioconductor.org/packages/XVector>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {XVector: Foundation of external vector representation and manipulation in
## Bioconductor},
## author = {Hervé Pagès and Patrick Aboyoun},
## year = {2024},
## note = {R package version 0.44.0},
## url = {https://bioconductor.org/packages/XVector},
## doi = {10.18129/B9.bioc.XVector},
## }
##
## ATTENTION: This citation information has been auto-generated from the
## package DESCRIPTION file and may need manual editing, see
## 'help("citation")'.
##
## [[83]]
## To cite package 'BiocGenerics' in publications use:
##
## Orchestrating high-throughput genomic analysis with Bioconductor. W.
## Huber, V.J. Carey, R. Gentleman, ..., M. Morgan Nature Methods,
## 2015:12, 115.
##
## A BibTeX entry for LaTeX users is
##
## @Article{,
## author = {{Huber} and {W.} and {Carey} and V. J. and {Gentleman} and {R.} and {Anders} and {S.} and {Carlson} and {M.} and {Carvalho} and B. S. and {Bravo} and H. C. and {Davis} and {S.} and {Gatto} and {L.} and {Girke} and {T.} and {Gottardo} and {R.} and {Hahne} and {F.} and {Hansen} and K. D. and {Irizarry} and R. A. and {Lawrence} and {M.} and {Love} and M. I. and {MacDonald} and {J.} and {Obenchain} and {V.} and {{Ole's}} and A. K. and {{Pag`es}} and {H.} and {Reyes} and {A.} and {Shannon} and {P.} and {Smyth} and G. K. and {Tenenbaum} and {D.} and {Waldron} and {L.} and {Morgan} and {M.}},
## title = {{O}rchestrating high-throughput genomic analysis with {B}ioconductor},
## journal = {Nature Methods},
## year = {2015},
## volume = {12},
## number = {2},
## pages = {115--121},
## url = {http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html},
## }
##
## [[84]]
## To cite package 'foreach' in publications use:
##
## Microsoft, Weston S (2022). _foreach: Provides Foreach Looping
## Construct_. R package version 1.5.2,
## <https://CRAN.R-project.org/package=foreach>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {foreach: Provides Foreach Looping Construct},
## author = {{Microsoft} and Steve Weston},
## year = {2022},
## note = {R package version 1.5.2},
## url = {https://CRAN.R-project.org/package=foreach},
## }
##
## [[85]]
## To cite package 'pillar' in publications use:
##
## Müller K, Wickham H (2023). _pillar: Coloured Formatting for
## Columns_. R package version 1.9.0,
## <https://CRAN.R-project.org/package=pillar>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {pillar: Coloured Formatting for Columns},
## author = {Kirill Müller and Hadley Wickham},
## year = {2023},
## note = {R package version 1.9.0},
## url = {https://CRAN.R-project.org/package=pillar},
## }
##
## [[86]]
## To cite package 'yulab.utils' in publications use:
##
## Yu G (2024). _yulab.utils: Supporting Functions for Packages
## Maintained by 'YuLab-SMU'_. R package version 0.1.5,
## <https://CRAN.R-project.org/package=yulab.utils>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {yulab.utils: Supporting Functions for Packages Maintained by 'YuLab-SMU'},
## author = {Guangchuang Yu},
## year = {2024},
## note = {R package version 0.1.5},
## url = {https://CRAN.R-project.org/package=yulab.utils},
## }
##
## [[87]]
## The 'splines' package is part of R. To cite R in publications use:
##
## R Core Team (2024). _R: A Language and Environment for Statistical
## Computing_. R Foundation for Statistical Computing, Vienna, Austria.
## <https://www.R-project.org/>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {R: A Language and Environment for Statistical Computing},
## author = {{R Core Team}},
## organization = {R Foundation for Statistical Computing},
## address = {Vienna, Austria},
## year = {2024},
## url = {https://www.R-project.org/},
## }
##
## We have invested a lot of time and effort in creating R, please cite it
## when using it for data analysis. See also 'citation("pkgname")' for
## citing R packages.
##
## [[88]]
## To cite treeio in publications use:
##
## Guangchuang Yu. (2022). Data Integration, Manipulation and
## Visualization of Phylogenetic Trees (1st edition). Chapman and
## Hall/CRC.
##
## LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR
## Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package
## for phylogenetic tree input and output with richly annotated and
## associated data. Molecular Biology and Evolution 2020, 37(2):599-603.
## doi: 10.1093/molbev/msz240
##
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.
##
## [[89]]
## To cite package 'survival' in publications use:
##
## Therneau T (2024). _A Package for Survival Analysis in R_. R package
## version 3.7-0, <https://CRAN.R-project.org/package=survival>.
##
## Terry M. Therneau, Patricia M. Grambsch (2000). _Modeling Survival
## Data: Extending the Cox Model_. Springer, New York. ISBN
## 0-387-98784-3.
##
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.
##
## [[90]]
## To cite package 'tidyselect' in publications use:
##
## Henry L, Wickham H (2024). _tidyselect: Select from a Set of
## Strings_. R package version 1.2.1,
## <https://CRAN.R-project.org/package=tidyselect>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {tidyselect: Select from a Set of Strings},
## author = {Lionel Henry and Hadley Wickham},
## year = {2024},
## note = {R package version 1.2.1},
## url = {https://CRAN.R-project.org/package=tidyselect},
## }
##
## [[91]]
## To cite package 'Biostrings' in publications use:
##
## Pagès H, Aboyoun P, Gentleman R, DebRoy S (2024). _Biostrings:
## Efficient manipulation of biological strings_.
## doi:10.18129/B9.bioc.Biostrings
## <https://doi.org/10.18129/B9.bioc.Biostrings>, R package version
## 2.72.1, <https://bioconductor.org/packages/Biostrings>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {Biostrings: Efficient manipulation of biological strings},
## author = {Hervé Pagès and Patrick Aboyoun and Robert Gentleman and Saikat DebRoy},
## year = {2024},
## note = {R package version 2.72.1},
## url = {https://bioconductor.org/packages/Biostrings},
## doi = {10.18129/B9.bioc.Biostrings},
## }
##
## [[92]]
## To cite package 'knitr' in publications use:
##
## Xie Y (2024). _knitr: A General-Purpose Package for Dynamic Report
## Generation in R_. R package version 1.48, <https://yihui.org/knitr/>.
##
## Yihui Xie (2015) Dynamic Documents with R and knitr. 2nd edition.
## Chapman and Hall/CRC. ISBN 978-1498716963
##
## Yihui Xie (2014) knitr: A Comprehensive Tool for Reproducible
## Research in R. In Victoria Stodden, Friedrich Leisch and Roger D.
## Peng, editors, Implementing Reproducible Computational Research.
## Chapman and Hall/CRC. ISBN 978-1466561595
##
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.
##
## [[93]]
## To cite package 'gridExtra' in publications use:
##
## Auguie B (2017). _gridExtra: Miscellaneous Functions for "Grid"
## Graphics_. R package version 2.3,
## <https://CRAN.R-project.org/package=gridExtra>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
## author = {Baptiste Auguie},
## year = {2017},
## note = {R package version 2.3},
## url = {https://CRAN.R-project.org/package=gridExtra},
## }
##
## [[94]]
## To cite phyloseq in publications, or otherwise credit, please use:
##
## phyloseq: An R package for reproducible interactive analysis and
## graphics of microbiome census data. Paul J. McMurdie and Susan Holmes
## (2013) PLoS ONE 8(4):e61217.
##
## A BibTeX entry for LaTeX users is
##
## @Article{,
## author = {Paul J. McMurdie and Susan Holmes},
## journal = {PLoS ONE},
## pages = {e61217},
## title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
## volume = {8},
## number = {4},
## year = {2013},
## url = {http://dx.plos.org/10.1371/journal.pone.0061217},
## }
##
## [[95]]
## To cite package 'IRanges' in publications use:
##
## Lawrence M, Huber W, Pag\`es H, Aboyoun P, Carlson M, et al. (2013)
## Software for Computing and Annotating Genomic Ranges. PLoS Comput
## Biol 9(8): e1003118. doi:10.1371/journal.pcbi.1003118
##
## A BibTeX entry for LaTeX users is
##
## @Article{,
## title = {Software for Computing and Annotating Genomic Ranges},
## author = {Michael Lawrence and Wolfgang Huber and Herv\'e Pag\`es and Patrick Aboyoun and Marc Carlson and Robert Gentleman and Martin Morgan and Vincent Carey},
## year = {2013},
## journal = {{PLoS} Computational Biology},
## volume = {9},
## issue = {8},
## doi = {10.1371/journal.pcbi.1003118},
## url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118},
## }
##
## [[96]]
## To cite zCompositions in publications, please use:
##
## Palarea-Albaladejo J, Martín-Fernández JA (2015). "zCompositions - R
## package for multivariate imputation of left-censored data under a
## compositional approach." _Chemometrics and Intelligent Laboratory
## Systems_, *143*, 85-96. doi:10.1016/j.chemolab.2015.02.019
## <https://doi.org/10.1016/j.chemolab.2015.02.019>.
##
## A BibTeX entry for LaTeX users is
##
## @Article{,
## title = {zCompositions -- R package for multivariate imputation of left-censored data under a compositional approach},
## author = {J. Palarea-Albaladejo and J. A. Martín-Fernández},
## journal = {Chemometrics and Intelligent Laboratory Systems},
## year = {2015},
## volume = {143},
## pages = {85--96},
## doi = {10.1016/j.chemolab.2015.02.019},
## }
##
## [[97]]
## The 'stats4' package is part of R. To cite R in publications use:
##
## R Core Team (2024). _R: A Language and Environment for Statistical
## Computing_. R Foundation for Statistical Computing, Vienna, Austria.
## <https://www.R-project.org/>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {R: A Language and Environment for Statistical Computing},
## author = {{R Core Team}},
## organization = {R Foundation for Statistical Computing},
## address = {Vienna, Austria},
## year = {2024},
## url = {https://www.R-project.org/},
## }
##
## We have invested a lot of time and effort in creating R, please cite it
## when using it for data analysis. See also 'citation("pkgname")' for
## citing R packages.
##
## [[98]]
## To cite package 'xfun' in publications use:
##
## Xie Y (2024). _xfun: Supporting Functions for Packages Maintained by
## 'Yihui Xie'_. R package version 0.46,
## <https://CRAN.R-project.org/package=xfun>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {xfun: Supporting Functions for Packages Maintained by 'Yihui Xie'},
## author = {Yihui Xie},
## year = {2024},
## note = {R package version 0.46},
## url = {https://CRAN.R-project.org/package=xfun},
## }
##
## [[99]]
## To cite package 'Biobase' in publications use:
##
## Orchestrating high-throughput genomic analysis with Bioconductor. W.
## Huber, V.J. Carey, R. Gentleman, ..., M. Morgan Nature Methods,
## 2015:12, 115.
##
## A BibTeX entry for LaTeX users is
##
## @Article{,
## author = {W. Huber and V. J. Carey and R. Gentleman and S. Anders and M. Carlson and B. S. Carvalho and H. C. Bravo and S. Davis and L. Gatto and T. Girke and R. Gottardo and F. Hahne and K. D. Hansen and R. A. Irizarry and M. Lawrence and M. I. Love and J. MacDonald and V. Obenchain and A. K. {Ole's} and H. {Pag`es} and A. Reyes and P. Shannon and G. K. Smyth and D. Tenenbaum and L. Waldron and M. Morgan},
## title = {{O}rchestrating high-throughput genomic analysis with {B}ioconductor},
## journal = {Nature Methods},
## year = {2015},
## volume = {12},
## number = {2},
## pages = {115--121},
## url = {http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html},
## }
##
## [[100]]
## To cite package 'DT' in publications use:
##
## Xie Y, Cheng J, Tan X (2024). _DT: A Wrapper of the JavaScript
## Library 'DataTables'_. R package version 0.33,
## <https://CRAN.R-project.org/package=DT>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
## author = {Yihui Xie and Joe Cheng and Xianying Tan},
## year = {2024},
## note = {R package version 0.33},
## url = {https://CRAN.R-project.org/package=DT},
## }
##
## [[101]]
## To cite stringi in publications, use:
##
## Gagolewski M (2022). "stringi: Fast and portable character string
## processing in R." _Journal of Statistical Software_, *103*(2), 1-59.
## doi:10.18637/jss.v103.i02 <https://doi.org/10.18637/jss.v103.i02>.
##
## A BibTeX entry for LaTeX users is
##
## @Article{,
## title = {{stringi}: {F}ast and portable character string processing in {R}},
## author = {Marek Gagolewski},
## journal = {Journal of Statistical Software},
## year = {2022},
## volume = {103},
## number = {2},
## pages = {1--59},
## doi = {10.18637/jss.v103.i02},
## }
##
## [[102]]
## To cite package 'UCSC.utils' in publications use:
##
## Pagès H (2024). _UCSC.utils: Low-level utilities to retrieve data
## from the UCSC Genome Browser_. doi:10.18129/B9.bioc.UCSC.utils
## <https://doi.org/10.18129/B9.bioc.UCSC.utils>, R package version
## 1.0.0, <https://bioconductor.org/packages/UCSC.utils>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {UCSC.utils: Low-level utilities to retrieve data from the UCSC Genome
## Browser},
## author = {Hervé Pagès},
## year = {2024},
## note = {R package version 1.0.0},
## url = {https://bioconductor.org/packages/UCSC.utils},
## doi = {10.18129/B9.bioc.UCSC.utils},
## }
##
## [[103]]
## To cite package 'ggfun' in publications use:
##
## Yu G, Xu S (2024). _ggfun: Miscellaneous Functions for 'ggplot2'_. R
## package version 0.1.5, <https://CRAN.R-project.org/package=ggfun>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {ggfun: Miscellaneous Functions for 'ggplot2'},
## author = {Guangchuang Yu and Shuangbin Xu},
## year = {2024},
## note = {R package version 0.1.5},
## url = {https://CRAN.R-project.org/package=ggfun},
## }
##
## [[104]]
## To cite package 'lazyeval' in publications use:
##
## Wickham H (2019). _lazyeval: Lazy (Non-Standard) Evaluation_. R
## package version 0.2.2, <https://CRAN.R-project.org/package=lazyeval>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {lazyeval: Lazy (Non-Standard) Evaluation},
## author = {Hadley Wickham},
## year = {2019},
## note = {R package version 0.2.2},
## url = {https://CRAN.R-project.org/package=lazyeval},
## }
##
## [[105]]
## To cite package 'yaml' in publications use:
##
## Garbett SP, Stephens J, Simonov K, Xie Y, Dong Z, Wickham H, Horner
## J, reikoch, Beasley W, O'Connor B, Warnes GR, Quinn M, Kamvar ZN, Gao
## C (2024). _yaml: Methods to Convert R Data to YAML and Back_. R
## package version 2.3.10, <https://CRAN.R-project.org/package=yaml>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {yaml: Methods to Convert R Data to YAML and Back},
## author = {Shawn P Garbett and Jeremy Stephens and Kirill Simonov and Yihui Xie and Zhuoer Dong and Hadley Wickham and Jeffrey Horner and {reikoch} and Will Beasley and Brendan O'Connor and Gregory R. Warnes and Michael Quinn and Zhian N. Kamvar and Charlie Gao},
## year = {2024},
## note = {R package version 2.3.10},
## url = {https://CRAN.R-project.org/package=yaml},
## }
##
## ATTENTION: This citation information has been auto-generated from the
## package DESCRIPTION file and may need manual editing, see
## 'help("citation")'.
##
## [[106]]
## To cite package 'evaluate' in publications use:
##
## Wickham H, Xie Y (2024). _evaluate: Parsing and Evaluation Tools that
## Provide More Details than the Default_. R package version 0.24.0,
## <https://CRAN.R-project.org/package=evaluate>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {evaluate: Parsing and Evaluation Tools that Provide More Details than the
## Default},
## author = {Hadley Wickham and Yihui Xie},
## year = {2024},
## note = {R package version 0.24.0},
## url = {https://CRAN.R-project.org/package=evaluate},
## }
##
## [[107]]
## To cite package 'codetools' in publications use:
##
## Tierney L (2024). _codetools: Code Analysis Tools for R_. R package
## version 0.2-20, <https://CRAN.R-project.org/package=codetools>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {codetools: Code Analysis Tools for R},
## author = {Luke Tierney},
## year = {2024},
## note = {R package version 0.2-20},
## url = {https://CRAN.R-project.org/package=codetools},
## }
##
## ATTENTION: This citation information has been auto-generated from the
## package DESCRIPTION file and may need manual editing, see
## 'help("citation")'.
##
## [[108]]
## To cite package 'ggplotify' in publications use:
##
## Yu G (2023). _ggplotify: Convert Plot to 'grob' or 'ggplot' Object_.
## R package version 0.1.2,
## <https://CRAN.R-project.org/package=ggplotify>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {ggplotify: Convert Plot to 'grob' or 'ggplot' Object},
## author = {Guangchuang Yu},
## year = {2023},
## note = {R package version 0.1.2},
## url = {https://CRAN.R-project.org/package=ggplotify},
## }
##
## [[109]]
## To cite package 'cli' in publications use:
##
## Csárdi G (2024). _cli: Helpers for Developing Command Line
## Interfaces_. R package version 3.6.3,
## <https://CRAN.R-project.org/package=cli>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {cli: Helpers for Developing Command Line Interfaces},
## author = {Gábor Csárdi},
## year = {2024},
## note = {R package version 3.6.3},
## url = {https://CRAN.R-project.org/package=cli},
## }
##
## [[110]]
## To cite package 'rpart' in publications use:
##
## Therneau T, Atkinson B (2023). _rpart: Recursive Partitioning and
## Regression Trees_. R package version 4.1.23,
## <https://CRAN.R-project.org/package=rpart>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {rpart: Recursive Partitioning and Regression Trees},
## author = {Terry Therneau and Beth Atkinson},
## year = {2023},
## note = {R package version 4.1.23},
## url = {https://CRAN.R-project.org/package=rpart},
## }
##
## [[111]]
## To cite package 'munsell' in publications use:
##
## Wickham C (2024). _munsell: Utilities for Using Munsell Colours_. R
## package version 0.5.1, <https://CRAN.R-project.org/package=munsell>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {munsell: Utilities for Using Munsell Colours},
## author = {Charlotte Wickham},
## year = {2024},
## note = {R package version 0.5.1},
## url = {https://CRAN.R-project.org/package=munsell},
## }
##
## ATTENTION: This citation information has been auto-generated from the
## package DESCRIPTION file and may need manual editing, see
## 'help("citation")'.
##
## [[112]]
## To cite package 'jquerylib' in publications use:
##
## Sievert C, Cheng J (2021). _jquerylib: Obtain 'jQuery' as an HTML
## Dependency Object_. R package version 0.1.4,
## <https://CRAN.R-project.org/package=jquerylib>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {jquerylib: Obtain 'jQuery' as an HTML Dependency Object},
## author = {Carson Sievert and Joe Cheng},
## year = {2021},
## note = {R package version 0.1.4},
## url = {https://CRAN.R-project.org/package=jquerylib},
## }
##
## [[113]]
## To cite package 'Rcpp' in publications use:
##
## Eddelbuettel D, Francois R, Allaire J, Ushey K, Kou Q, Russell N,
## Ucar I, Bates D, Chambers J (2024). _Rcpp: Seamless R and C++
## Integration_. R package version 1.0.13,
## <https://CRAN.R-project.org/package=Rcpp>.
##
## Eddelbuettel D, François R (2011). "Rcpp: Seamless R and C++
## Integration." _Journal of Statistical Software_, *40*(8), 1-18.
## doi:10.18637/jss.v040.i08 <https://doi.org/10.18637/jss.v040.i08>.
##
## Eddelbuettel D (2013). _Seamless R and C++ Integration with Rcpp_.
## Springer, New York. doi:10.1007/978-1-4614-6868-4
## <https://doi.org/10.1007/978-1-4614-6868-4>, ISBN 978-1-4614-6867-7.
##
## Eddelbuettel D, Balamuta J (2018). "Extending R with C++: A Brief
## Introduction to Rcpp." _The American Statistician_, *72*(1), 28-36.
## doi:10.1080/00031305.2017.1375990
## <https://doi.org/10.1080/00031305.2017.1375990>.
##
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.
##
## [[114]]
## To cite package 'GenomeInfoDb' in publications use:
##
## Arora S, Morgan M, Carlson M, Pagès H (2024). _GenomeInfoDb:
## Utilities for manipulating chromosome names, including modifying them
## to follow a particular naming style_.
## doi:10.18129/B9.bioc.GenomeInfoDb
## <https://doi.org/10.18129/B9.bioc.GenomeInfoDb>, R package version
## 1.40.1, <https://bioconductor.org/packages/GenomeInfoDb>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {GenomeInfoDb: Utilities for manipulating chromosome names, including modifying
## them to follow a particular naming style},
## author = {Sonali Arora and Martin Morgan and Marc Carlson and Hervé Pagès},
## year = {2024},
## note = {R package version 1.40.1},
## url = {https://bioconductor.org/packages/GenomeInfoDb},
## doi = {10.18129/B9.bioc.GenomeInfoDb},
## }
##
## [[115]]
## The 'parallel' package is part of R. To cite R in publications use:
##
## R Core Team (2024). _R: A Language and Environment for Statistical
## Computing_. R Foundation for Statistical Computing, Vienna, Austria.
## <https://www.R-project.org/>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {R: A Language and Environment for Statistical Computing},
## author = {{R Core Team}},
## organization = {R Foundation for Statistical Computing},
## address = {Vienna, Austria},
## year = {2024},
## url = {https://www.R-project.org/},
## }
##
## We have invested a lot of time and effort in creating R, please cite it
## when using it for data analysis. See also 'citation("pkgname")' for
## citing R packages.
##
## [[116]]
## To cite package 'mvtnorm' in publications use:
##
## Genz A, Bretz F (2009). _Computation of Multivariate Normal and t
## Probabilities_, series Lecture Notes in Statistics. Springer-Verlag,
## Heidelberg. ISBN 978-3-642-01688-2.
##
## A BibTeX entry for LaTeX users is
##
## @Book{,
## title = {Computation of Multivariate Normal and t Probabilities},
## author = {Alan Genz and Frank Bretz},
## series = {Lecture Notes in Statistics},
## year = {2009},
## publisher = {Springer-Verlag},
## address = {Heidelberg},
## isbn = {978-3-642-01688-2},
## }
##
## [[117]]
## To cite package 'scales' in publications use:
##
## Wickham H, Pedersen T, Seidel D (2023). _scales: Scale Functions for
## Visualization_. R package version 1.3.0,
## <https://CRAN.R-project.org/package=scales>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {scales: Scale Functions for Visualization},
## author = {Hadley Wickham and Thomas Lin Pedersen and Dana Seidel},
## year = {2023},
## note = {R package version 1.3.0},
## url = {https://CRAN.R-project.org/package=scales},
## }
##
## [[118]]
## To cite package 'crayon' in publications use:
##
## Csárdi G (2024). _crayon: Colored Terminal Output_. R package version
## 1.5.3, <https://CRAN.R-project.org/package=crayon>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {crayon: Colored Terminal Output},
## author = {Gábor Csárdi},
## year = {2024},
## note = {R package version 1.5.3},
## url = {https://CRAN.R-project.org/package=crayon},
## }
##
## [[119]]
## To cite package 'rlang' in publications use:
##
## Henry L, Wickham H (2024). _rlang: Functions for Base Types and Core
## R and 'Tidyverse' Features_. R package version 1.1.4,
## <https://CRAN.R-project.org/package=rlang>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {rlang: Functions for Base Types and Core R and 'Tidyverse' Features},
## author = {Lionel Henry and Hadley Wickham},
## year = {2024},
## note = {R package version 1.1.4},
## url = {https://CRAN.R-project.org/package=rlang},
## }
##
## [[120]]
## Please cite the multcomp package by the following reference:
##
## Hothorn T, Bretz F, Westfall P (2008). "Simultaneous Inference in
## General Parametric Models." _Biometrical Journal_, *50*(3), 346-363.
##
## A BibTeX entry for LaTeX users is
##
## @Article{,
## title = {Simultaneous Inference in General Parametric Models},
## author = {Torsten Hothorn and Frank Bretz and Peter Westfall},
## journal = {Biometrical Journal},
## year = {2008},
## volume = {50},
## number = {3},
## pages = {346--363},
## }2 Data Import
JEB00020<-read_excel("JEB00020.xlsx")
JEB00423<-read_excel("JEB00423.xlsx")
BRB<-read_excel("BRB.xlsx")
DBP<-read_excel("DBP.xlsx")
GTDB_taxonomy<-read_excel("GTDB_taxonomy.xlsx")
Bisanz_strain<-read_excel("Bisanz_strain.xlsx")
straintree <- read.tree("RAxML_bestTree.faas_refined.tre")3 Fig. 4a BRB effect on bacterial strain growth
Pvalue <- BRB%>%
group_by(metric,StrainID) %>%
do(
wilcox.test(.$value ~ .$Concentration) %>%
broom::tidy()
) %>%
ungroup() %>%
mutate(FDR=p.adjust(p.value, method="BH"))
Pvalue %>% interactive_table()summarized_curve_data <- BRB%>%
group_by(StrainID, Concentration, metric) %>%
reframe(mean_value = mean(value)) %>%
ungroup() %>%
group_by(StrainID, metric) %>%
summarize(delta = mean_value[Concentration == "Drug"] - mean_value[Concentration == "Vehicle"], log2FC = log2((mean_value[Concentration == "Drug"])/(mean_value[Concentration == "Vehicle"])))3.1 FDR<=0.05 and log2FC>=0.5
FDR<-
BRB %>%
group_by(metric,StrainID) %>%
do(
wilcox.test(.$value ~ .$Concentration) %>%
broom::tidy()
) %>%
ungroup() %>%
mutate(FDR=p.adjust(p.value, method="BH")) %>%
filter(metric=="k"|metric=="r"|metric=="t_mid") %>%
filter(FDR<0.05)
summarized_curve_data %>%
filter(metric=="k"|metric=="r"|metric=="t_mid") %>%
filter(log2FC>0.5|log2FC<(-0.5)) %>%
filter(StrainID %in% FDR$StrainID)%>%
interactive_table()3.2 Tree
tree_heatmap_table <- summarized_curve_data %>%
mutate(StrainID = gsub("_IS","", StrainID)) %>%
left_join(GTDB_taxonomy[,c("StrainID", "Phylum", "GTDB_Species")]) %>%
dplyr::select(-delta) %>%
filter(!metric == "t_max") %>%
pivot_wider(id_cols = c("StrainID", "Phylum", "GTDB_Species"), names_from = "metric", values_from = "log2FC") %>%
left_join(Bisanz_strain) %>%
mutate(StrainID=Species)
#straintree with species name
t_label<-
straintree$tip.label %>%
as.data.frame()
t_species <- t_label%>%
mutate(StrainID=t_label$`.`) %>%
left_join(Bisanz_strain) %>%
dplyr::select(Species)
straintree$tip.label = t_species$Species
## Joining with `by = join_by(StrainID)`
filtered_straintree <- drop.tip(straintree, straintree$tip.label[!straintree$tip.label %in% tree_heatmap_table$StrainID])
filtered_straintree<-root(filtered_straintree, outgroup = "Akkermansia muciniphila JEB00423") #root on Akkermansia muciniphila JEB00423
tree_metadata <- tree_heatmap_table %>%
filter(StrainID %in% filtered_straintree$tip.label)
tree_heatmap_table <- tree_heatmap_table %>%
filter(StrainID %in% filtered_straintree$tip.label) %>%
dplyr::select(-Phylum, -GTDB_Species,-Species) %>%
column_to_rownames("StrainID") %>%
mutate(k=as.numeric(k))%>%
mutate(r=as.numeric(r))%>%
mutate(t_mid=as.numeric(-t_mid))3.3 Color Pallettes
plot_colors <- list()
plot_colors$Phylum_colors <- c("Pseudomonadota" = "aquamarine3","Actinomycetota" = "firebrick","Bacteroidota" = "olivedrab","Verrucomicrobiota" = "gold","Bacillota_A" = "darkorchid","Bacillota" = "steelblue2","Bacillota_C" = "darkblue","Fusobacteriota" = "darkorange","Spirochaetota" = "chartreuse2")3.4 StrainID
# Add Phylum Labels and Start Tree
p <- ggtree(filtered_straintree, layout="rectangular") %<+% tree_metadata + geom_tiplab(aes(color = Phylum)) +
scale_color_manual(values = plot_colors$Phylum_colors, na.value = "gray90", name = "Phylum")
# Add heatmap
p2 <- gheatmap(p, data = tree_heatmap_table, offset = .5, width=0.3, low = "white", high = "darkred", color = "white", colnames = TRUE, font.size=3, colnames_position= "top", colnames_angle = 0, colnames_offset_y = 0, hjust = 0) +
scale_fill_gradient2(na.value = "gray90", high = "darkred", low = "darkblue",name = paste0("log2 Fold Change (log2(Drug/Veh))")) +
xlim(NA,4)
p2
4 Fig. 4b DBP effect on bacterial strain growth
Pvalue <- DBP%>%
group_by(metric,StrainID) %>%
do(
wilcox.test(.$value ~ .$Concentration) %>%
broom::tidy()
) %>%
ungroup() %>%
mutate(FDR=p.adjust(p.value, method="BH"))
Pvalue %>% interactive_table()summarized_curve_data <- DBP%>%
group_by(StrainID, Concentration, metric) %>%
reframe(mean_value = mean(value)) %>%
ungroup() %>%
group_by(StrainID, metric) %>%
summarize(delta = mean_value[Concentration == "Drug"] - mean_value[Concentration == "Vehicle"], log2FC = log2((mean_value[Concentration == "Drug"])/(mean_value[Concentration == "Vehicle"])))4.1 FDR<=0.05 and log2FC>=0.5
FDR<-
DBP %>%
group_by(metric,StrainID) %>%
do(
wilcox.test(.$value ~ .$Concentration) %>%
broom::tidy()
) %>%
ungroup() %>%
mutate(FDR=p.adjust(p.value, method="BH")) %>%
filter(metric=="k"|metric=="r"|metric=="t_mid") %>%
filter(FDR<0.05)
summarized_curve_data %>%
filter(metric=="k"|metric=="r"|metric=="t_mid") %>%
filter(log2FC>0.5|log2FC<(-0.5)) %>%
filter(StrainID %in% FDR$StrainID)%>%
interactive_table()4.2 Tree
tree_heatmap_table <- summarized_curve_data %>%
mutate(StrainID = gsub("_IS","", StrainID)) %>%
left_join(GTDB_taxonomy[,c("StrainID", "Phylum", "GTDB_Species")]) %>%
dplyr::select(-delta) %>%
filter(!metric == "t_max") %>%
pivot_wider(id_cols = c("StrainID", "Phylum", "GTDB_Species"), names_from = "metric", values_from = "log2FC") %>%
left_join(Bisanz_strain) %>%
mutate(StrainID=Species)
## Joining with `by = join_by(StrainID)`
filtered_straintree <- drop.tip(straintree, straintree$tip.label[!straintree$tip.label %in% tree_heatmap_table$StrainID])
filtered_straintree<-root(filtered_straintree, outgroup = "Akkermansia muciniphila JEB00423") #root on Akkermansia muciniphila JEB00423
tree_metadata <- tree_heatmap_table %>%
filter(StrainID %in% filtered_straintree$tip.label)
tree_heatmap_table <- tree_heatmap_table %>%
filter(StrainID %in% filtered_straintree$tip.label) %>%
dplyr::select(-Phylum, -GTDB_Species,-Species) %>%
column_to_rownames("StrainID") %>%
mutate(k=as.numeric(k))%>%
mutate(r=as.numeric(r))%>%
mutate(t_mid=as.numeric(-t_mid))4.3 StrainID
# Add Phylum Labels and Start Tree
p <- ggtree(filtered_straintree, layout="rectangular") %<+% tree_metadata + geom_tiplab(aes(color = Phylum)) +
scale_color_manual(values = plot_colors$Phylum_colors, na.value = "gray90", name = "Phylum")
# Add heatmap
p2 <- gheatmap(p, data = tree_heatmap_table, offset = .5, width=0.3, low = "white", high = "darkred", color = "white", colnames = TRUE, font.size=3, colnames_position= "top", colnames_angle = 0, colnames_offset_y = 0, hjust = 0) +
scale_fill_gradient2(na.value = "gray90", high = "darkred", low = "darkblue",name = paste0("log2 Fold Change (log2(Drug/Veh))")) +
xlim(NA,4)
p2
5 Fig. S2a A.muciniphila JEB00020 growth curve
JEB00020 %>%
ggplot(aes(x=time, y=ODnorm, fill=Trt,group=Trt))+
stat_summary(geom="ribbon", alpha=0.5) +
xlab("Time (hours)")
6 Fig. S2b A.muciniphila JEB00423 growth curve
JEB00423 %>%
ggplot(aes(x=time, y=ODnorm, fill=Trt,group=Trt))+
stat_summary(geom="ribbon", alpha=0.5) +
xlab("Time (hours)")